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<meta name="author" content="Chen Tong" />
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<li class="chapter" data-level="2.1" data-path="plot.html"><a href="plot.html#boxplot"><i class="fa fa-check"></i><b>2.1</b> Boxplot</a></li>
<li class="chapter" data-level="2.2" data-path="plot.html"><a href="plot.html#flower"><i class="fa fa-check"></i><b>2.2</b> Flower</a></li>
<li class="chapter" data-level="2.3" data-path="plot.html"><a href="plot.html#line-plot"><i class="fa fa-check"></i><b>2.3</b> Line plot</a></li>
<li class="chapter" data-level="2.4" data-path="plot.html"><a href="plot.html#pretty-heatmap"><i class="fa fa-check"></i><b>2.4</b> Pretty heatmap</a></li>
<li class="chapter" data-level="2.5" data-path="plot.html"><a href="plot.html#volcano-plot"><i class="fa fa-check"></i><b>2.5</b> Volcano plot</a></li>
<li class="chapter" data-level="2.6" data-path="plot.html"><a href="plot.html#venndiagram-plot"><i class="fa fa-check"></i><b>2.6</b> VennDiagram plot</a></li>
<li class="chapter" data-level="2.7" data-path="plot.html"><a href="plot.html#enrichment-plot"><i class="fa fa-check"></i><b>2.7</b> Enrichment plot</a></li>
<li class="chapter" data-level="2.8" data-path="plot.html"><a href="plot.html#upsetview-plot"><i class="fa fa-check"></i><b>2.8</b> Upsetview plot</a></li>
<li class="chapter" data-level="2.9" data-path="plot.html"><a href="plot.html#scatter-plot"><i class="fa fa-check"></i><b>2.9</b> Scatter plot</a></li>
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<li class="chapter" data-level="2.11" data-path="plot.html"><a href="plot.html#histogram"><i class="fa fa-check"></i><b>2.11</b> Histogram</a></li>
<li class="chapter" data-level="2.12" data-path="plot.html"><a href="plot.html#eulerdiagrams-plot"><i class="fa fa-check"></i><b>2.12</b> EulerDiagrams plot</a></li>
<li class="chapter" data-level="2.13" data-path="plot.html"><a href="plot.html#non-classical-venn"><i class="fa fa-check"></i><b>2.13</b> Non-classical venn</a></li>
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<li class="chapter" data-level="3.1" data-path="analysis.html"><a href="analysis.html#wgcna"><i class="fa fa-check"></i><b>3.1</b> WGCNA</a></li>
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            <section class="normal" id="section-">
<div id="plot" class="section level1 hasAnchor" number="2">
<h1><span class="header-section-number">2</span> Plot<a href="plot.html#plot" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<div id="boxplot" class="section level2 hasAnchor" number="2.1">
<h2><span class="header-section-number">2.1</span> Boxplot<a href="plot.html#boxplot" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Both <code>wide matrix</code> and <code>long matrix</code> data can be used to draw boxplot. In the demo1, we used the gene expression table in different samples with long matrix format and the metadata table of samples.</p>
<p>In the drawing parameters:</p>
<ul>
<li><p>Specify the x-axis to display group information by selecting the option of <code>conditions</code> in the <code>X-axis variable</code> parameter;</p></li>
<li><p>Specify the y-axis to display the expression of genes in different samples by selecting the option of <code>ENSG00000109689</code> in the <code>Y-axis variable</code> parameter;</p></li>
<li><p>Add lines of the paired samples in the two groups by selecting the option of <code>individual</code> in the <code>Group variable for lining points</code> parameter;</p></li>
<li><p>Use the color set “Set3” to color the boxes of two groups by selecting the option of <code>Set3</code> in the <code>Manual color vector (color set)</code> parameter;</p></li>
<li><p>The <code>Do statistics significane test for each group</code> parameter is selected as <code>yes</code> so that a letter is added to the top of the box to show whether the gene is significantly different between the two groups.</p></li>
</ul>
<p><img src="http://www.ehbio.com/Cloud_Platform/Picture_list/Boxplot_demo1.png" /></p>
</div>
<div id="flower" class="section level2 hasAnchor" number="2.2">
<h2><span class="header-section-number">2.2</span> Flower<a href="plot.html#flower" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>In the demo1, paste two-column matrix with the sample information of genes.</p>
<p>In the drawing parameters:</p>
<ul>
<li><p>Specify the column containing genes by selecting the option of <code>Gene</code> in the <code>Column containing all items</code> parameter;</p></li>
<li><p>Specify the column containing sample information by selecting the option of <code>Sample</code> in the <code>Column containing all sets information</code> parameter;</p></li>
<li><p>Change the label of the center circle which reflecting the number of common genes of all samples by inputting <code>core</code> in the textarea of <code>Center circle label</code> parameter.</p></li>
</ul>
<p><img src="http://www.ehbio.com/Cloud_Platform/Picture_list/flower_demo1.png" /></p>
</div>
<div id="line-plot" class="section level2 hasAnchor" number="2.3">
<h2><span class="header-section-number">2.3</span> Line plot<a href="plot.html#line-plot" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Both <code>wide matrix</code> and <code>long matrix</code> data can be used to draw line plot. In the demo1, we used the gene expression table in different samples with wide matrix format.</p>
<p>In the drawing parameters:</p>
<p>Use the color set “Set3” to color the lines of genes by selecting the option of <code>Set3</code> in the <code>Manual color vector (color set)</code> parameter.</p>
<p><img src="http://www.ehbio.com/Cloud_Platform/Picture_list/line_demo1.png" /></p>
</div>
<div id="pretty-heatmap" class="section level2 hasAnchor" number="2.4">
<h2><span class="header-section-number">2.4</span> Pretty heatmap<a href="plot.html#pretty-heatmap" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>In the demo1, we used the common gene expression profile which contains the expression of genes in different samples.</p>
<p>In the drawing parameters:</p>
<ul>
<li><p>The <code>Duplicate rownames</code> parameter is selected as <code>Automatically rename</code> to deal with duplicate row names of data;</p></li>
<li><p>The <code>Scale data</code> parameter is selected as <code>Raw</code> to scale the rows of data for clustering and visualization;</p></li>
<li><p>Use the color set “Set3” to color the lines of genes by selecting the option of <code>Set3</code> in the <code>Manual color vector (color set)</code> parameter.</p></li>
</ul>
<p><img src="http://www.ehbio.com/Cloud_Platform/Picture_list/pheatmap_demo1.png" /></p>
</div>
<div id="volcano-plot" class="section level2 hasAnchor" number="2.5">
<h2><span class="header-section-number">2.5</span> Volcano plot<a href="plot.html#volcano-plot" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>In the demo1, we used the different gene analysis result incluing all gene name, the mean of gene expression between the two groups, log2 fold change of gene expression in the two groups, statistical significance results, some interesting gene names, and the information whether the gene is different between the two groups.</p>
<p>In the drawing parameters:</p>
<ul>
<li><p>Specify the name of the column whose value is log2 fold change of gene expression in the two groups by selecting the option of <code>log2FoldChange</code> in the <code>Fold change column</code> parameter;</p></li>
<li><p>Specify the name of the column whose value is statistical significance results by selecting the option of <code>padj</code> in the <code>Statistical significance column</code> parameter;</p></li>
<li><p>The <code>Log10 transform significance value</code> parameter is selected as <code>Log 10 transform</code> to transform log10 on the statistical significance results;</p></li>
<li><p>Specify the name of the column whose value is the information whether the gene is different in the two groups by selecting the option of <code>Level</code> in the <code>Gene expression change status variable</code> parameter;</p></li>
<li><p>After selecting the option of <code>Level</code> in the <code>Gene expression change status variable</code> parameter, the order of variables in the <code>level</code> can be set by selecting the order of the options of the <code>Status variable order</code> parameter;</p></li>
<li><p>Change the color transparency of points by inputting <code>0.4</code> in the textarea of <code>Color transparency</code> parameter;</p></li>
<li><p>Add the horizontal lines to show the significance threshold by inputting <code>fdr</code> in the textarea of <code>Horizontal line positions</code> parameter;</p></li>
<li><p>Add the horizontal and vertical lines to show the threshold of significance and log2 fold change by inputting <code>0.05,1</code> in the textarea of <code>DE genes filtering threshold</code> parameter. And if <code>Gene expression change status variable</code> parameter is empty, the parameter will automatically determine which genes are the different between the two groups based on the provided thresholds.</p></li>
</ul>
<p><img src="http://www.ehbio.com/Cloud_Platform/Picture_list/volcano_demo1.png" /></p>
</div>
<div id="venndiagram-plot" class="section level2 hasAnchor" number="2.6">
<h2><span class="header-section-number">2.6</span> VennDiagram plot<a href="plot.html#venndiagram-plot" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>In the demo1, paste two-column matrix with the sample information of genes.</p>
<p>In the drawing parameters:</p>
<ul>
<li><p>Specify the column containing genes by selecting the option of <code>Gene</code> in the <code>Column containing all items</code> parameter;</p></li>
<li><p>Specify the column containing sample information by selecting the option of <code>Sample</code> in the <code>Column containing all sets information</code> parameter;</p></li>
<li><p>Samples of interest and order of presentation can be set by selecting <code>Set1, Set2, Set3, Set4</code> (multiple options in order) of the <code>Choose which sets to plot and their order</code> parameter;</p></li>
<li><p>Change the label size by inputting <code>0.6</code> in the textarea of <code>Label size</code> parameter;</p></li>
<li><p>Change the blank range around the diagram by inputting <code>0.1</code> in the textarea of <code>Margins</code> parameter.</p></li>
</ul>
<p><img src="http://www.ehbio.com/Cloud_Platform/Picture_list/VennDiagram_demo1.png" /></p>
</div>
<div id="enrichment-plot" class="section level2 hasAnchor" number="2.7">
<h2><span class="header-section-number">2.7</span> Enrichment plot<a href="plot.html#enrichment-plot" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>In the demo1, paste four-column matrix with the group information, GeneRatio, statistical significance results, the number of genes of GO terms, and the description of GO terms.</p>
<p>In the drawing parameters:</p>
<ul>
<li><p>Specify the x-axis to display GeneRatio by selecting the option of <code>geneRatio</code> in the <code>X-axis variable</code> parameter;</p></li>
<li><p>Specify the y-axis to display the description of GO terms by selecting the option of <code>Description</code> in the <code>Y-axis variable</code> parameter;</p></li>
<li><p>Specify the color of points to display the statistical significance results by selecting the option of <code>Qvalue</code> in the <code>Color variable</code> parameter;</p></li>
<li><p>Neg log10 transform statistical significance results by selecting the option of <code>Qvalue</code> in the <code>Neg log10 transform variable</code> parameter;</p></li>
<li><p>Specify the size of points to display the number of genes of GO terms by selecting the option of <code>Count</code> in the <code>Point size variable</code> parameter;</p></li>
<li><p>Specify the shape of points to display the group information by selecting the option of <code>SampleGroup</code> in the <code>Shape variable</code> parameter.</p></li>
</ul>
<p><img src="http://www.ehbio.com/Cloud_Platform/Picture_list/enrichment_demo1.png" /></p>
</div>
<div id="upsetview-plot" class="section level2 hasAnchor" number="2.8">
<h2><span class="header-section-number">2.8</span> Upsetview plot<a href="plot.html#upsetview-plot" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Both <code>wide matrix</code> and <code>long matrix with header</code> data can be used to draw upsetview plot. In the demo1, paste wide matrix containing the name of movies and the style of movies.</p>
<p>In the drawing parameters:</p>
<p>Specify the threshold of intersections to plot by inputting <code>7</code> in the textarea of the <code>Number of intersections to show</code> parameter.</p>
<p><img src="http://www.ehbio.com/Cloud_Platform/Picture_list/upsetview_demo1.png" /></p>
</div>
<div id="scatter-plot" class="section level2 hasAnchor" number="2.9">
<h2><span class="header-section-number">2.9</span> Scatter plot<a href="plot.html#scatter-plot" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>In the demo1, paste four-column matrix with gene names, the sample information, gene expression, and gene percent.</p>
<ul>
<li><p>Specify the x-axis to display gene by selecting the option of <code>Gene</code> in the <code>X-axis variable</code> parameter;</p></li>
<li><p>Specify the y-axis to display the sample information by selecting the option of <code>Cluster</code> in the <code>Y-axis variable</code> parameter;</p></li>
<li><p>Change the color of points to display the gene expression by selecting the option of <code>Expr</code> in the <code>Color variable</code> parameter;</p></li>
<li><p>Add the label of points to display the gene expression by selecting the option of <code>Expr</code> in the <code>Point size variable</code> parameter;</p></li>
<li><p>Change the size of points to display the gene percent by selecting the option of <code>Percent</code> in the <code>Size variable</code> parameter;</p></li>
<li><p>The <code>Legend position</code> parameter is selected as <code>Top</code> to put the legend above the graph.</p></li>
</ul>
<p><img src="http://www.ehbio.com/Cloud_Platform/Picture_list/scatter_demo1.png" /></p>
</div>
<div id="bar-plot" class="section level2 hasAnchor" number="2.10">
<h2><span class="header-section-number">2.10</span> Bar plot<a href="plot.html#bar-plot" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Both <code>wide matrix</code> and <code>long matrix</code> data can be used to draw bar plot. In the demo1, we used the gene expression table in different samples with long matrix format.</p>
<ul>
<li><p>Specify the x-axis to display sample information by selecting the option of <code>ID</code> in the <code>X-axis variable</code> parameter;</p></li>
<li><p>Specify the y-axis to display the expression of genes in different samples by selecting the option of <code>Expression</code> in the <code>Y-axis variable</code> parameter;</p></li>
<li><p>Change the color of points to display the gene expression by selecting the option of <code>Gene</code> in the <code>Color variable</code> parameter;</p></li>
<li><p>The <code>Add text</code> parameter is selected as <code>True</code> so that the texts are added to bars to display the gene expressions;</p></li>
<li><p>Change the font size by inputting <code>10</code> in the textarea of <code>Base font size</code> parameter;</p></li>
<li><p>Use the color set “Set3” to color the bars by selecting the option of <code>Set3</code> in the <code>Manual color vector (color set)</code> parameter.</p></li>
</ul>
<p><img src="http://www.ehbio.com/Cloud_Platform/Picture_list/Bar_demo1.png" /></p>
</div>
<div id="histogram" class="section level2 hasAnchor" number="2.11">
<h2><span class="header-section-number">2.11</span> Histogram<a href="plot.html#histogram" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Both <code>wide matrix</code> and <code>long matrix</code> data can be used to draw histogram. In the demo1, we used a data which is the weight in different genders with long matrix format.</p>
<p>In the drawing parameters:</p>
<ul>
<li><p>Specify the x-axis to display weight by selecting the option of <code>weight</code> in the <code>X-axis variable</code> parameter;</p></li>
<li><p>Use the gender as group information by selecting the option of <code>sex</code> in the <code>Group variable</code> parameter;</p></li>
<li><p>Specify the y-axis to display the density of weight by selecting the option of <code>Density</code> in the <code>Y-axis variable</code> parameter;</p></li>
<li><p>The graph is composed of histogram and density curve by selecting the option of <code>Line and Histogram</code> in the <code>Plot type</code> parameter;</p></li>
<li><p><code>Fill areas</code> parameter is selecting as <code>True</code> to fill the plot with colors;</p></li>
<li><p><code>Vline at mean value</code> parameter is selecting as <code>True</code> to add vertical lines for each group.</p></li>
</ul>
<p><img src="http://www.ehbio.com/Cloud_Platform/Picture_list/histogram_demo1.png" /></p>
</div>
<div id="eulerdiagrams-plot" class="section level2 hasAnchor" number="2.12">
<h2><span class="header-section-number">2.12</span> EulerDiagrams plot<a href="plot.html#eulerdiagrams-plot" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>In the demo1, paste two-column matrix with the sample information of genes.</p>
<p>In the drawing parameters:</p>
<ul>
<li><p>The <code>Specified input format</code> parameter need to be selected as <code>Items</code> due to the need to count the number of genes in different sets;</p></li>
<li><p>Specify the column containing genes by selecting the option of <code>Gene</code> in the <code>Column containing all items</code> parameter;</p></li>
<li><p>Specify the column containing sample information by selecting the option of <code>Sample</code> in the <code>Column containing all sets information</code> parameter;</p></li>
<li><p>Set <code>Plot type</code> parameter to <code>Counts</code> to add the number of genes in different sets;</p></li>
<li><p>Set <code>Plot shape</code> parameter to <code>Circle</code> to make the graph corresponding to all groups circular;</p></li>
<li><p>Change the font size for numbers by inputting <code>1</code> in the textarea of <code>Font size for numbers</code> parameter;</p></li>
<li><p>Change the font size for labels by inputting <code>1</code> in the textarea of <code>Font size for labels</code> parameter;</p></li>
<li><p>Set <code>Line type</code> parameter to <code>Soild</code> to make the edge of the graph the solid lines;</p></li>
<li><p>Change the color transparency of points by inputting <code>0.6</code> in the textarea of <code>Color transparency</code> parameter.</p></li>
</ul>
<p><img src="http://www.ehbio.com/Cloud_Platform/Picture_list/euler_demo1.png" /></p>
</div>
<div id="non-classical-venn" class="section level2 hasAnchor" number="2.13">
<h2><span class="header-section-number">2.13</span> Non-classical venn<a href="plot.html#non-classical-venn" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>In the demo1, paste two-column matrix with the sample information of genes.</p>
<p>In the drawing parameters:</p>
<ul>
<li><p>Specify the column containing genes by selecting the option of <code>Gene</code> in the <code>Column containing all items</code> parameter;</p></li>
<li><p>Specify the column containing sample information by selecting the option of <code>Sample</code> in the <code>Column containing all sets information</code> parameter;</p></li>
<li><p>Specify the interest samples to display by selecting the option of <code>Set1, Set2, Set3</code> in the <code>Select sets to show</code> parameter;</p></li>
<li><p>The <code>Do weighted</code> parameter is selected as <code>No</code> so that do not calculate the weight of the data;</p></li>
<li><p>The <code>Venn type</code> parameter is selected as <code>Triangles</code> so that each set is displayed as a triangle and combined into a triangle;</p></li>
<li><p>The <code>Show the set label</code> parameter is selected as <code>True</code> so that each set is displayed as a triangle and combines into a triangle;</p></li>
<li><p>Add the sample name on the graph by selecting <code>True</code> in the <code>Show the set label</code> parameter;</p></li>
<li><p>Fill the sets with colors by selecting <code>True</code> in the <code>Fill set</code> parameter;</p></li>
<li><p>Add the sample boundaries on the graph by selecting <code>True</code> in the <code>Show boundaries of the Sets</code> parameter;</p></li>
<li><p>Add the elements information of different sets on the graph by selecting <code>Elements</code> in the <code>FaceText</code> parameter.</p></li>
</ul>
<p><img src="http://www.ehbio.com/Cloud_Platform/Picture_list/VennDiagram2_demo1.png" /></p>

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